All Known Implementing Classes:

AbstractFeature, FeatureDbReferenceInfo, QualityFeature, QuantityFeature, TextFeature
```
public interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
```
Interface class to handle describing arbitrary features. A feature can be found at multiple locations in a sequence such as the surface of a protein where different sequence positions make up that feature. Ligand binding pocket is another example. The location in its current form knows the start and stop position in a sequence and thus should contain knowledge about the actual sequence. A feature can contain features to handle cases where a domain is a feature and the secondary structures covered by that domain and other requirements for grouping.

Author:

Scooter Willis , Paolo Pavan

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`void`	`addQualifier(String key, Qualifier qualifier)`	Add a qualifier
`List<FeatureInterface<S,C>>`	`getChildrenFeatures()`	Get the features contained by this feature
`String`	`getDescription()`	Get the description that can be used to describe the feature
`AbstractLocation`	`getLocations()`	The location(s) of this feature where the location should contain a reference to parent and sequence etc.
`FeatureInterface<S,C>`	`getParentFeature()`	Get the parent feature
`Map<String,List<Qualifier>>`	`getQualifiers()`	Get the qualifiers for this feature
`String`	`getShortDescription()`	Get the short description that can be used to describe the feature
`String`	`getSource()`	The source of the feature.
`String`	`getType()`	The type of the feature.
`Object`	`getUserObject()`
`void`	`setChildrenFeatures(List<FeatureInterface<S,C>> features)`	Set the children features
`void`	`setDescription(String description)`	Set the description that can be used to describe the feature
`void`	`setLocation(AbstractLocation loc)`	The new location for this feature.
`void`	`setParentFeature(FeatureInterface<S,C> feature)`	Set the parent feature
`void`	`setQualifiers(Map<String,List<Qualifier>> qualifiers)`	Set the qualifiers
`void`	`setShortDescription(String shortDescription)`	Set the short description that can be used to describe the feature
`void`	`setSource(String source)`	Change the source of the FeatureInterface.
`void`	`setType(String type)`	Change the type of this feature.
`void`	`setUserObject(Object userObject)`

- Method Detail
  - getShortDescription
```
String getShortDescription()
```
    Get the short description that can be used to describe the feature
    
    Returns:
  - setShortDescription
```
void setShortDescription(String shortDescription)
```
    Set the short description that can be used to describe the feature
    
    Parameters:
    
    shortDescription -
  - getDescription
```
String getDescription()
```
    Get the description that can be used to describe the feature
    
    Returns:
  - setDescription
```
void setDescription(String description)
```
    Set the description that can be used to describe the feature
  - getLocations
```
AbstractLocation getLocations()
```
    The location(s) of this feature where the location should contain a reference to parent and sequence etc.
    The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.
    
    Returns:
    
    a Location anchoring this feature
  - setLocation
```
void setLocation(AbstractLocation loc)
```
    The new location for this feature.
    The location may be complicated or simply a range. The annotation is assumed to apply to the entire region contained within the location. Any values returned from methods that rely on the old location must not be affected.
    
    Parameters:
    
    loc - the new Location for this feature
  - getType
```
String getType()
```
    The type of the feature.
    
    Returns:
    
    the type of this sequence
  - setType
```
void setType(String type)
```
    Change the type of this feature.
    
    Parameters:
    
    type - new type String
  - getSource
```
String getSource()
```
    The source of the feature. This may be a program or process.
    
    Returns:
    
    the source, or generator
  - setSource
```
void setSource(String source)
```
    Change the source of the FeatureInterface.
    
    Parameters:
    
    source - the new source String
  - setParentFeature
```
void setParentFeature(FeatureInterface<S,C> feature)
```
    Set the parent feature
    
    Parameters:
    
    feature -
  - getParentFeature
```
FeatureInterface<S,C> getParentFeature()
```
    Get the parent feature
    
    Returns:
  - getChildrenFeatures
```
List<FeatureInterface<S,C>> getChildrenFeatures()
```
    Get the features contained by this feature
    
    Returns:
  - setChildrenFeatures
```
void setChildrenFeatures(List<FeatureInterface<S,C>> features)
```
    Set the children features
    
    Parameters:
    
    features -
  - getUserObject
```
Object getUserObject()
```
    Returns:
    
    the userObject
  - setUserObject
```
void setUserObject(Object userObject)
```
    Parameters:
    
    userObject - the userObject to set
  - getQualifiers
```
Map<String,List<Qualifier>> getQualifiers()
```
    Get the qualifiers for this feature
    
    Returns:
  - setQualifiers
```
void setQualifiers(Map<String,List<Qualifier>> qualifiers)
```
    Set the qualifiers
    
    Parameters:
    
    qualifiers -
  - addQualifier
```
void addQualifier(String key,
                  Qualifier qualifier)
```
    Add a qualifier
    
    Parameters:
    
    qualifier -

Interface FeatureInterface<S extends AbstractSequence<C>,​C extends Compound>

Method Summary

Method Detail

getShortDescription

setShortDescription

getDescription

setDescription

getLocations

setLocation

getType

setType

getSource

setSource

setParentFeature

getParentFeature

getChildrenFeatures

setChildrenFeatures

getUserObject

setUserObject

getQualifiers

setQualifiers

addQualifier

Interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>